[gmx-users] Simulation of membrane protein

[James Starlight]

Justin, hello!

In the algorthm presented in the tutorial there is one inconvenience that is
many iterations of the shrinking/minimization of the protein ( e.g if i'd
like to obrain good value for S per lipid for my structure). Is there any
way to make this process automated ? ( e.g some program wich could do all of
those operations untill defined value for some magnitudes would be reached )

Also I'd like to ask about g_membed. As I've understood for that program I
need in merged pdb struture ( consist of my peptide inserted in the membrane
) as well as merged topology. Is there any way to prepare this data exept
the way presented in your tutorial ? (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html)

E.g I've heard that this could also be done via PyMol. Where I could find
example of such preparation ?


Thanks for your help,
James

2011/10/15 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>> Dear Gromacs's users!
>>
>>
>> I'd like to simulate some membrane proteins in their native environment.
>>
>> Recently I've found a good tutotial of the same simulation of the KALP
>> peptide in DPPC membrane (http://www.bevanlab.biochem.**
>> vt.edu/Pages/Personal/justin/**gmx-tutorials/membrane_**
>> protein/index.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>
>> ).
>>
>> Is there  someone who have also tried to make thit tutorial ?
>>
>
> Yes, per our server logs, several hundred people have :)
>
>
>  First of all its very intresting for me the positioning of the protein in
>> the membrane via specific  perl script called infrategro. What values for
>> the cutoff radius as well as measurements of  the area per lipid  are most
>> adequate for different membrane proteins?
>>
>>
> The ones given in the tutorial work quite well.  They are the defaults
> suggested by the developers of InflateGRO.
>
>
>  Could you also tell me some alternative ways of full algorithm of the
>> protein insertion in the membrane?
>>
>>
>>
> Careful use of genbox (but will require significantly more equilibration as
> there will be large gaps), or g_membed.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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